József Geml


I am a biologist with special interest in microbial community ecology. More specifically, I use high-throughput DNA sequencing to study how abiotic and biotic factors influence the diversity, composition, and function of soil and plant micrbiomes, e.g., along elevation gradients, climate change experiments, and forest successional stages, as well as in response to various land use types and to invasive species.


Arctic, bacteria, climate change, forest ecology, fungi. DNA metabarcoding, land use, microbial ecology, tropical ecology


My motivation for research has always been the desire to explore, document, and conserve the richness of nature, particularly its biological diversity. Recently, I have become increasingly concerned about the loss of natural habitats and biodiversity, which threatens the very survival of humans as well.

The common pattern emerging from my studies in arctic, temperate and tropical biomes is that many fungi are specific to certain habitats and that fungal communities respond very rapidly to environmental disturbance. Therefore, fungi are ideally suited to be bio-indicators of “soil health” and can help us to choose more sustainable land use practices.

Fungi in the Andean cloud forests
Sampling soil fungi in the Atacama Desert


  • Fungal community composition along elevation gradients in tropical mountains
  • Assessing the effects of environmental factors on microbial communities at landscape level
  • Microbial diversity and community assembly in primary and regenerating secondary tropical forests
  • Evaluating the effect of climate change on the composition and functionality of arctic microbial communities 
  • Fungal evolution, molecular systematics, and phylogeography


  • Geml J. 2019. Soil fungal communities reflect aspect-driven environmental structuring and vegetation types in a Pannonian forest landscape. Fungal Ecology 39:63-79.
  • Varga T, Krizsán K, Földi Cs., ... Geml J ... et al. 2019. Megaphylogeny resolves global patterns of mushroom evolution. Nature Ecology and Evolution 3:668-678.
  • Geml J, Morgado LN, Semenova-Nelsen TA, Schilthuizen M. 2017. Changes in richness and community composition of ectomycorrhizal fungi among altitudinal vegetation types on Mount Kinabalu in Borneo. New Phytologist. 215:454-468.
  • Geml J, Semenova TA, Morgado LN, Welker JM. 2016. Changes in composition and abundance of functional groups of arctic fungi in response to long-term summer warming. Biology Letters 12:20160503
  • Morgado LN, Semenova TA, Welker JM, Walker MD, Smets E, Geml J. 2016. Long-term increase in snow depth leads to compositional changes in arctic ectomycorrhizal fungal communities. Global Change Biology  22:3080-3096.
  • Geml J, Pastor N, Fernandez L, Pacheco S, Semenova TA, Becerra AG, Wicaksono CY, Nouhra ER. 2014. Large-scale fungal diversity assessment in the Andean Yungas forests reveals strong community turnover among forest types along an altitudinal gradient. Molecular Ecology 23:2452-2472.
  • Geml J, Timling I, Robinson CH, Lennon N, Nusbaum HC, Brochmann C, Noordeloos ME, Taylor DL. 2012. An arctic community of symbiotic fungi assembled by long-distance dispersers: phylogenetic diversity of ectomycorrhizal basidiomycetes in Svalbard based on soil and sporocarp DNA. Journal of Biogeography 39:74-88.
  • Geml J, Laursen GA, Herriott I, McFarland JM, Booth MG, Lennon N, Nusbaum HC, Taylor DL. 2010. Phylogenetic and ecological analyses of soil and sporocarp DNA sequences reveal high diversity and strong habitat partitioning in the boreal ectomycorrhizal genus Russula Pers. (Russulales; Basidiomycota). New Phytologist 187:494-507.
  • Geml J, Kauff F, Brochmann C, Taylor DL. 2010. Surviving climate changes: High genetic diversity and transoceanic gene flow in two arctic-alpine lichens, Flavocetraria cucullata and F. nivalis (Parmeliaceae, Ascomycota) Journal of Biogeography 37:1529-1542.
  • Geml J, Tulloss RE, Laursen GA, Sazanova NA, Taylor DL. 2008. Evidence for strong inter- and intracontinental phylogeographic structure in Amanita muscaria, a wind-dispersed ectomycorrhizal basidiomycete. Molecular Phylogenetics and Evolution 48:694-701.


Current and former Ph.D. students

    • PhD. Student M. Polling (U Leiden, 2018-) (co-supervised)
    • PhD. student N. Pastor (UN Córdoba, 2013-) (co-supervised)
    • PhD. student T.A. Semenova (U. Leiden 2012-2016)
    • PhD. student L.N. Morgado (U. Leiden 2011-2016)
    Climate change experiments in Toolik Field Staton, Alaska


    • Integrated Taxonomy MS. course (U Leiden, 2017-)
    • Methods in Biodiversity Assessment MS. course (U Leiden, 2016-)
    • Tropical Biodiversity MS. field course (U Leiden, 2014-)
    • Tree of Life: Biodiversity of Plants, Protists and Fungi (U Leiden, 2012-)

    In the